Man Drew, you are having the exact same problem as me! I pulled my heads and my gaskets were fine BTW. Nothing out of the ordinary there. I have narrowed it down to a plugged radiator. After I pulled the radiator and ran a hose through it it took a bit for water to start coming out the other side. Pull the radiator and go to Ace Hardware and get some Muriatic Acid. Pour it in the radiator and let it sit for awhile then flush it out with fresh water. Do that a few times and it should flow better. Probably not your problem since it was fine before the intake install, but wouldn't hurt. Total cost for the acid is like $4.00.
Did you route your serpentine belt the correct way around your water pump? If not and it's running backwards that could be the problem. I have no idea really as I am in the same situation as you now I think. We'll see when I get everything back together.
Good luck man. If you need any help let me know. I gotta pull my cam tomorrow and that'll only take a few, so after that I will be free for a couple days.
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